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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-03-01 to 2022-03-31 by month" --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_*.csv
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_ethnicity.csv
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/input*.csv
generate_study_population_practice_count:
run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --index-date-range "2019-03-01 to 2022-03-31 by month" --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_practice_count_*.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/measure_*_rate.csv
calculate_rates:
run: python:latest python analysis/rate_calculations.py
needs: [generate_measures]
outputs:
moderately_sensitive:
tables: output/rate_table_*.csv
plots: output/plot_*.png
decile_chart: output/decile_chart.png
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/qof_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [calculate_rates, generate_study_population_practice_count]
outputs:
moderately_sensitive:
notebook: output/qof_notebook.html
# Asthma register (ast_reg)
generate_study_population_ast_reg:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_ast_reg
--index-date-range "2021-04-01 to 2022-03-01 by month"
--output-dir=output
--output-format=csv
outputs:
highly_sensitive:
cohort: output/input_ast_reg*.csv
join_ethnicity_ast_reg:
run: >
cohort-joiner:v0.0.12
--lhs output/input_ast*.csv
--rhs output/input_ethnicity*.csv
--output-dir output/joined
needs: [generate_study_population_ethnicity, generate_study_population_ast_reg]
outputs:
highly_sensitive:
cohort: output/joined/input_ast*.csv
generate_measures_ast_reg:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_ast_reg
--output-dir=output/joined
needs: [join_ethnicity_ast_reg]
outputs:
moderately_sensitive:
measure_csv: output/joined/measure_ast_reg_*_rate.csv